"The decision on the agriculture minister's resignation is welcome. I hope that this will provide a good basis for constructive cooperation with the government and the Seimas," she said in a comment forwarded to BNS by her press office.
Grybauskaitė earlier this month called on Markauskas to leave his post.
"I think such a minister has neither the political nor moral right to stay in his post. He has lost it," she said in an interview with LRT Radio several weeks ago.
The president then said that the minister's reputation would harm Lithuania's image in EU negotiations on agriculture financing after 2020.
"If the head of government and the ruling majority think that such a minister is suitable for them, then I'm very sorry that we have such a ruling majority," she added.
Prime Minister Saulius Skvernelis said in response that he would not yield to pressure from the president, adding that he would wait for law-enforcement bodies' findings on Markauskas' farming business before making his own decision regarding the minister.
Skvernelis said after the Cabinet's meeting on Wednesday that Markauskas was stepping down amid criticism over his family's farming practices.
The prime minister underlined that the minister's decision to resign was important for the stability of the government and the state.
Markauskas came under fire after the 15min.lt news website reported that his family had used several plots of land without the landowners' permission and had received EU payments for that land.
The minister says that his family farmed the land under oral arrangements with the landowners.
In its response to an inquiry from the opposition Homeland Union–Lithuanian Christian Democrats, the Lithuanian Financial Crime Investigation Service (FNTT) said on Tuesday that it had found no signs of criminal activity in the farming practices of Markauskas or his mother, Sofija Markauskienė.
However, the minister's family could have violated crop declaration rules for obtaining EU payments, FNNT said.
Skvernelis said on Wednesday that Markauskas was not facing any charges from law-enforcement bodies, but the requirements for an agriculture minister are higher than those for an ordinary farmer.
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